Try the Firefox Safe Mode to see how it works there. The Safe Mode is a troubleshooting mode, which disables most add-ons.

(If you're not using it, switch to the Default theme.)

You can open the Firefox 4.0+ Safe Mode by holding the Shift key when you use the Firefox desktop or Start menu shortcut.

Or use the Help menu item and click on the Restart with Add-ons Disabled... menu item while Firefox is running.

Don't select anything right now, just use "'Start in Safe Mode"To exit the Firefox Safe Mode, just close Firefox and wait a few seconds before using the Firefox shortcut (without the Shift key) to open it again.If it is good in the Firefox Safe Mode, your problem is probably caused by an extension, and you need to figure out which one.

I had a similar problem were links within a pdf document were being corrupted, so that the linked to document was not found when the link was clicked on. The problem only occurred in Firefox and not in any other browser.
The nightly build didn't help me, and neither did downloading the latest version of the PDF viewer. But the problem was solved by going to options and changing the pdf viewer to "Use Adobe Acrobat (in firefox)" from "Use Adobe Acrobat (default)".